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Andreas Gammelgaard Damsbo 2025-06-26 12:36:48 +02:00
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inst/apps/FreesearchR/ui.R
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# ns <- NS(id)
ui_elements <- list(
##############################################################################
#########
######### Home panel
#########
##############################################################################
"home" = bslib::nav_panel(
title = "FreesearchR",
shiny::fluidRow(
shiny::column(width = 2),
shiny::column(
width = 8,
shiny::markdown(readLines("www/intro.md")),
shiny::column(width = 2)
)
),
icon = shiny::icon("home")
),
##############################################################################
#########
######### Import panel
#########
##############################################################################
"import" = bslib::nav_panel(
title = "Import",
shiny::fluidRow(
shiny::column(width = 2),
shiny::column(
width = 8,
shiny::h4("Choose your data source"),
shiny::br(),
shinyWidgets::radioGroupButtons(
inputId = "source",
selected = "file",
choices = c(
"File upload" = "file",
"REDCap server export" = "redcap",
"Local or sample data" = "env"
),
size = "lg"
),
shiny::tags$script('document.querySelector("#source div").style.width = "100%"'),
shiny::helpText("Upload a file from your device, get data directly from REDCap or select a sample data set for testing from the app."),
shiny::br(),
shiny::br(),
shiny::conditionalPanel(
condition = "input.source=='file'",
import_file_ui(
id = "file_import",
layout_params = "dropdown",
# title = "Choose a datafile to upload",
file_extensions = c(".csv", ".tsv", ".txt", ".xls", ".xlsx", ".rds", ".ods", ".dta")
)
),
shiny::conditionalPanel(
condition = "input.source=='redcap'",
m_redcap_readUI(
id = "redcap_import",
title = ""
)
),
shiny::conditionalPanel(
condition = "input.source=='env'",
import_globalenv_ui(id = "env", title = NULL)
),
shiny::conditionalPanel(
condition = "input.source=='redcap'",
DT::DTOutput(outputId = "redcap_prev")
),
shiny::conditionalPanel(
condition = "output.data_loaded == true",
shiny::br(),
shiny::br(),
shiny::h5("Specify variables to include"),
shiny::fluidRow(
shiny::column(
width = 6,
shiny::br(),
shiny::p("Filter by completeness threshold and manual selection:"),
shiny::br(),
shiny::br()
),
shiny::column(
width = 6,
shinyWidgets::noUiSliderInput(
inputId = "complete_cutoff",
label = NULL,
update_on = "end",
min = 0,
max = 100,
step = 5,
value = 70,
format = shinyWidgets::wNumbFormat(decimals = 0),
color = datamods:::get_primary_color()
),
shiny::helpText("Exclude variables with completeness below the specified percentage."),
shiny::br(),
shiny::br(),
shiny::uiOutput(outputId = "import_var"),
shiny::uiOutput(outputId = "data_info_import", inline = TRUE)
)
)
),
shiny::br(),
shiny::br(),
shiny::actionButton(
inputId = "act_start",
label = "Start",
width = "100%",
icon = shiny::icon("play"),
disabled = TRUE
),
shiny::helpText('After importing, hit "Start" or navigate to the desired tab.'),
shiny::br(),
shiny::br(),
shiny::column(width = 2)
)
)
),
##############################################################################
#########
######### Data overview panel
#########
##############################################################################
"overview" =
# bslib::nav_panel_hidden(
bslib::nav_panel(
# value = "overview",
title = "Data",
bslib::navset_bar(
fillable = TRUE,
bslib::nav_panel(
title = "Overview",
tags$h3("Overview and filtering"),
fluidRow(
shiny::column(
width = 9,
shiny::uiOutput(outputId = "data_info", inline = TRUE),
shiny::tags$p(
"Below is a short summary table, on the right you can click to browse data and create data filters."
)
)
),
fluidRow(
shiny::column(
width = 9,
data_summary_ui(id = "data_summary")
),
shiny::column(
width = 3,
shiny::actionButton(
inputId = "modal_browse",
label = "Browse data",
width = "100%",
disabled = TRUE
),
shiny::tags$br(),
shiny::tags$br(),
shiny::uiOutput(outputId = "column_filter"),
shiny::helpText("Variable ", tags$a(
"data type",
href = "https://agdamsbo.github.io/FreesearchR/articles/data-types.html",
target = "_blank",
rel = "noopener noreferrer"
), " filtering."),
shiny::tags$br(),
shiny::tags$br(),
IDEAFilter::IDEAFilter_ui("data_filter"),
shiny::helpText("Observations level filtering."),
shiny::tags$br(),
shiny::tags$br()
)
),
shiny::tags$br(),
shiny::tags$br(),
shiny::tags$br(),
shiny::tags$br(),
shiny::tags$br()
),
bslib::nav_panel(
title = "Modify",
tags$h3("Subset, rename and convert variables"),
fluidRow(
shiny::column(
width = 9,
shiny::tags$p(
shiny::markdown("Below, are several options for simple data manipulation like update variables by renaming, creating new labels (for nicer tables in the report) and changing variable classes (numeric, factor/categorical etc.)."),
shiny::markdown("There are also more advanced options to modify factor/categorical variables as well as create new factor from a continous variable or new variables with *R* code. At the bottom you can restore the original data."),
shiny::markdown("Please note that data modifications are applied before any data or variable filtering is applied.")
)
)
),
# shiny::tags$br(),
update_variables_ui("modal_variables"),
shiny::tags$br(),
shiny::tags$br(),
shiny::tags$h4("Advanced data manipulation"),
shiny::tags$p("Below options allow more advanced varaible manipulations."),
shiny::tags$br(),
shiny::tags$br(),
shiny::fluidRow(
shiny::column(
width = 4,
shiny::actionButton(
inputId = "modal_update",
label = "Reorder factor levels",
width = "100%"
),
shiny::tags$br(),
shiny::helpText("Reorder the levels of factor/categorical variables."),
shiny::tags$br(),
shiny::tags$br()
),
shiny::column(
width = 4,
shiny::actionButton(
inputId = "modal_cut",
label = "New factor",
width = "100%"
),
shiny::tags$br(),
shiny::helpText("Create factor/categorical variable from a continous variable (number/date/time)."),
shiny::tags$br(),
shiny::tags$br()
),
shiny::column(
width = 4,
shiny::actionButton(
inputId = "modal_column",
label = "New variable",
width = "100%"
),
shiny::tags$br(),
shiny::helpText(shiny::markdown("Create a new variable/column based on an *R*-expression.")),
shiny::tags$br(),
shiny::tags$br()
)
),
tags$h4("Compare modified data to original"),
shiny::tags$br(),
shiny::tags$p(
"Raw print of the original vs the modified data."
),
shiny::tags$br(),
shiny::fluidRow(
shiny::column(
width = 6,
shiny::tags$b("Original data:"),
# verbatimTextOutput("original"),
shiny::verbatimTextOutput("original_str")
),
shiny::column(
width = 6,
shiny::tags$b("Modified data:"),
# verbatimTextOutput("modified"),
shiny::verbatimTextOutput("modified_str")
)
),
shiny::tags$br(),
shiny::actionButton(
inputId = "data_reset",
label = "Restore original data",
width = "100%"
),
shiny::tags$br(),
shiny::helpText("Reset to original imported dataset. Careful! There is no un-doing."),
shiny::tags$br()
)
)
),
##############################################################################
#########
######### Descriptive analyses panel
#########
##############################################################################
"describe" =
bslib::nav_panel(
title = "Evaluate",
id = "navdescribe",
bslib::navset_bar(
title = "",
sidebar = bslib::sidebar(
shiny::uiOutput(outputId = "data_info_nochar", inline = TRUE),
bslib::accordion(
open = "acc_chars",
multiple = FALSE,
bslib::accordion_panel(
value = "acc_chars",
title = "Characteristics",
icon = bsicons::bs_icon("table"),
shiny::uiOutput("strat_var"),
shiny::helpText("Only factor/categorical variables are available for stratification. Go back to the 'Data' tab to reclass a variable if it's not on the list."),
shiny::conditionalPanel(
condition = "input.strat_var!='none'",
shiny::radioButtons(
inputId = "add_p",
label = "Compare strata?",
selected = "no",
inline = TRUE,
choices = list(
"No" = "no",
"Yes" = "yes"
)
),
shiny::helpText("Option to perform statistical comparisons between strata in baseline table.")
),
shiny::br(),
shiny::br(),
shiny::actionButton(
inputId = "act_eval",
label = "Evaluate",
width = "100%",
icon = shiny::icon("calculator"),
disabled = TRUE
)
),
bslib::accordion_panel(
vlaue = "acc_cor",
title = "Correlations",
icon = bsicons::bs_icon("bounding-box"),
shiny::uiOutput("outcome_var_cor"),
shiny::helpText("To avoid evaluating the correlation of the outcome variable, this can be excluded from the plot or select 'none'."),
shiny::br(),
shinyWidgets::noUiSliderInput(
inputId = "cor_cutoff",
label = "Correlation cut-off",
min = 0,
max = 1,
step = .01,
value = .8,
format = shinyWidgets::wNumbFormat(decimals = 2),
color = datamods:::get_primary_color()
),
shiny::helpText("Set the cut-off for considered 'highly correlated'.")
)
)
),
bslib::nav_panel(
title = "Characteristics",
gt::gt_output(outputId = "table1")
),
bslib::nav_panel(
title = "Correlations",
data_correlations_ui(id = "correlations", height = 600)
)
)
),
##############################################################################
#########
######### Download panel
#########
##############################################################################
"visuals" = bslib::nav_panel(
title = "Visuals",
id = "navvisuals",
do.call(
bslib::navset_bar,
c(
data_visuals_ui("visuals"),
shiny::tagList(
bslib::nav_spacer(),
bslib::nav_item(
# shiny::img(shiny::icon("book")),
shiny::tags$a(
href = "https://agdamsbo.github.io/FreesearchR/articles/visuals.html",
"Notes (external)",
target = "_blank",
rel = "noopener noreferrer"
)
)
)
)
)
),
##############################################################################
#########
######### Regression analyses panel
#########
##############################################################################
"analyze" =
bslib::nav_panel(
title = "Regression",
id = "navanalyses",
do.call(
bslib::navset_bar,
regression_ui("regression")
)
),
##############################################################################
#########
######### Download panel
#########
##############################################################################
"download" =
bslib::nav_panel(
title = "Download",
id = "navdownload",
shiny::fluidRow(
shiny::column(width = 2),
shiny::column(
width = 8,
shiny::fluidRow(
shiny::column(
width = 6,
shiny::h4("Report"),
shiny::helpText("Choose your favourite output file format for further work, and download, when the analyses are done."),
shiny::br(),
shiny::br(),
shiny::selectInput(
inputId = "output_type",
label = "Output format",
selected = NULL,
choices = list(
"MS Word" = "docx",
"LibreOffice" = "odt"
# ,
# "PDF" = "pdf",
# "All the above" = "all"
)
),
shiny::br(),
# Button
shiny::downloadButton(
outputId = "report",
label = "Download report",
icon = shiny::icon("download")
)
# shiny::helpText("If choosing to output to MS Word, please note, that when opening the document, two errors will pop-up. Choose to repair and choose not to update references. The issue is being worked on. You can always choose LibreOffice instead."),
),
shiny::column(
width = 6,
shiny::h4("Data"),
shiny::helpText("Choose your favourite output data format to download the modified data."),
shiny::br(),
shiny::br(),
shiny::selectInput(
inputId = "data_type",
label = "Data format",
selected = NULL,
choices = list(
"R" = "rds",
"stata" = "dta",
"CSV" = "csv"
)
),
shiny::helpText("No metadata is saved when exporting to csv."),
shiny::br(),
shiny::br(),
# Button
shiny::downloadButton(
outputId = "data_modified",
label = "Download data",
icon = shiny::icon("download")
)
)
),
shiny::br(),
shiny::br(),
shiny::h4("Code snippets"),
shiny::tags$p("Below are the code bits used to create the final data set and the main analyses."),
shiny::tags$p("This can be used as a starting point for learning to code and for reproducibility."),
shiny::tagList(
lapply(
paste0("code_", c(
"import", "format", "data", "variables", "filter", "table1", "univariable", "multivariable"
)),
\(.x)shiny::htmlOutput(outputId = .x)
)
),
shiny::tags$br(),
shiny::br()
),
shiny::column(width = 2)
)
),
##############################################################################
#########
######### Documentation panel
#########
##############################################################################
"docs" = bslib::nav_item(
# shiny::img(shiny::icon("book")),
shiny::tags$a(
href = "https://agdamsbo.github.io/FreesearchR/",
"Docs (external)",
target = "_blank",
rel = "noopener noreferrer"
)
)
# bslib::nav_panel(
# title = "Documentation",
# # shiny::tags$iframe("www/docs.html", height=600, width=535),
# shiny::htmlOutput("docs_file"),
# shiny::br()
# )
)
# Initial attempt at creating light and dark versions
light <- custom_theme()
dark <- custom_theme(
bg = "#000",
fg = "#fff"
)
# Fonts to consider:
# https://webdesignerdepot.com/17-open-source-fonts-youll-actually-love/
ui_list <- shiny::tagList(
prismDependencies,
prismRDependency,
header_include(),
## This adds the actual favicon
## png and ico versions are kept for compatibility
shiny::tags$head(tags$link(rel="shortcut icon", href="favicon.svg")),
title = "FreesearchR",
theme = light,
shiny::useBusyIndicators(),
bslib::page_navbar(
id = "main_panel",
ui_elements$home,
ui_elements$import,
ui_elements$overview,
ui_elements$describe,
ui_elements$visuals,
ui_elements$analyze,
ui_elements$download,
bslib::nav_spacer(),
ui_elements$docs,
fillable = FALSE,
footer = shiny::tags$footer(
style = "background-color: #14131326; padding: 4px; text-align: center; bottom: 0; width: 100%;",
shiny::p(
style = "margin: 1",
"Data is only stored for analyses and deleted when the app is closed."
),
shiny::p(
style = "margin: 1; color: #888;",
shiny::tags$a("Docs", href = "https://agdamsbo.github.io/FreesearchR/", target = "_blank", rel = "noopener noreferrer")," | ", app_version(), " | ", shiny::tags$a("License: AGPLv3", href = "https://github.com/agdamsbo/FreesearchR/blob/main/LICENSE.md", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Source", href = "https://github.com/agdamsbo/FreesearchR/", target = "_blank", rel = "noopener noreferrer"), " | ", shiny::tags$a("Share feedback", href = "https://redcap.au.dk/surveys/?s=JPCLPTXYDKFA8DA8", target = "_blank", rel = "noopener noreferrer")
),
)
)
)
# ui_list <- shiny::tagAppendChild(ui_list,list(
# ## Basic Umami page tracking
# shiny::tags$head(includeHTML("www/umami-app.html"))
# # shiny::tags$head(shiny::tags$script(rel="defer", src="https://analytics.gdamsbo.dk/script.js", "data-website-id"="e7d4e13a-5824-4778-bbc0-8f92fb08303a"))
# ))
ui <- do.call(
bslib::page_fixed,ui_list)